Vibrio harveyi CAIM 1792 is a marine bacterial strain that causes mortalities in farmed shrimp in Northwest Mexico and the identification of virulence genes in this strain is important for understanding its pathogenicity. The aim of this work was to compare the V. harveyi CAIM 1792 genome with related genome sequences to determine their phylogenic relationship and explore unique regions in silico that differentiate this strain from other V. harveyi strains. Twenty-one newly sequenced genomes compared in silico against the CAIM 1792 genome at nucleotidic and predicted proteome levels. The proteome of CAIM 1792 had higher similarity to other V. harveyi strains (78%) than to the other closely related species Vibrio owensii (67%), Vibrio rotiferianus (63%), and Vibrio campbellii (59%). Pan-genome ORFans trees showed the best fit with the accepted phylogeny based on DDH and multilocus sequence analysis (MLSA) of 11 concatenated housekeeping genes. Single nucleotide polymorphisms (SNPs) analysis clustered 34/38 genomes within their accepted species. The pangenomic and SNP trees showed that V. harveyi is the most conserved of the four species studied and V. campbellii might be divided in at least three subspecies, supported by intergenomic distances analysis (GGDC). BLASTp atlases were created to identify unique regions among the most related genomes to V. harveyi CAIM 1792; these regions included genes encoding glycosyltransferases, specific type restriction modification systems, and a transcriptional regulator LysR reported to be involved in virulence, metabolism, quorum sensing, and motility.